Farm problems that persisted in the 1980's and a terrible drought in the summer of 1988 contributed to Dukakis winning.
As well as rural Whites being a lot more Democratic in 1988 in general.
In this part of the country, agriculture tends to be the foundation issue in elections. If things are good, then the party in power tends to be ok. In the 1980's many farmers in Iowa (and elsewhere) had severe financial problems and the democrats were able to pick up on that. A county swing map from 1980/1984 to 1988 would show that a broad swath from eastern NE/ND/SD into IL had sizable swings to the democrats. Fast forward to 2008: The lack of support for corn based ethanol hurt McCain badly in Iowa and northern IL and some of the eastern plains counties were the most democratic they have been since 1964. Iowa would have been far more competitive had McCain strongly supported ethanol and Obama would have won less counties in northern IL, SD, ND, and NE.